mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1379 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
9b00a45f21
commit
79b1603750
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@ -190,7 +190,11 @@ files if you compile with -DGZIP. It requires that your Unix support
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the "popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER,
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and -DPACK_MEMCPY options can make for faster parallel FFTs (in the
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PPPM solver) on some platforms. The -DPACK_ARRAY setting is the
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default.
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default. If you compile with -DLAMMPS_XDR, the build will include XDR
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compatability files for doing particle dumps in XTC format. This is
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only necessary if your platform does have its own XDR files available.
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See the Restrictions section of the <A HREF = "dump.html">dump</A> command for
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details.
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</P>
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<P>(8) The DEPFLAGS setting is how the C++ compiler creates a dependency
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file for each source file. This speeds re-compilation when source
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@ -185,7 +185,11 @@ files if you compile with -DGZIP. It requires that your Unix support
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the "popen" command. Using one of the -DPACK_ARRAY, -DPACK_POINTER,
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and -DPACK_MEMCPY options can make for faster parallel FFTs (in the
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PPPM solver) on some platforms. The -DPACK_ARRAY setting is the
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default.
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default. If you compile with -DLAMMPS_XDR, the build will include XDR
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compatability files for doing particle dumps in XTC format. This is
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only necessary if your platform does have its own XDR files available.
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See the Restrictions section of the "dump"_dump.html command for
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details.
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(8) The DEPFLAGS setting is how the C++ compiler creates a dependency
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file for each source file. This speeds re-compilation when source
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@ -30,8 +30,7 @@
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<PRE> <I>atom</I> args = none
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<I>bond</I> args = none
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<I>dcd</I> args = none
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<I>xtc</I> args = precision (optional)
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precision = power-of-10 value from 10 to 1000000 (default = 1000)
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<I>xtc</I> args = none
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<I>xyz</I> args = none
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<I>custom</I> args = list of atom attributes
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possible attributes = tag, mol, type,
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@ -138,16 +137,31 @@ below.
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<P>The <I>dcd</I> style writes DCD files, a standard atomic trajectory format
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used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
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files are binary and thus may not be portable to different machines.
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The dump group must be <I>all</I> for the <I>dcd</I> style.
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The dump group must be <I>all</I> for the <I>dcd</I> style. The <I>unwrap</I> option
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of the <A HREF = "dump_modify.html">dump_modify</A> command allows DCD coordinates
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to be written "unwrapped" by the image flags for each atom. Unwrapped
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means that if the atom has passed thru a periodic boundary one or more
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times, the value is printed for what the coordinate would be if it had
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not been wrapped back into the periodic box. Note that these
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coordinates may thus be far outside the box size stored with the
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snapshot.
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</P>
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<P>The <I>xtc</I> style writes XTC files, a compressed trajectory format used
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by the GROMACS molecular dynamics package, and described
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<A HREF = "http://www.gromacs.org/documentation/reference_3.3/online/xtc.html">here</A>.
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The precision used in XTC files can be specified; for example, a value
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of 100 means that coordinates are stored to 1/100 nanometer accuracy.
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XTC files are portable binary files written in the NFS XDR data
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format, so that any machine which supports XDR should be able to read
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them. The dump group must be <I>all</I> for the <I>xtc</I> style.
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The precision used in XTC files can be adjusted via the
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<A HREF = "dump_modify.html">dump_modify</A> command. The default value of 1000
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means that coordinates are stored to 1/1000 nanometer accuracy. XTC
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files are portable binary files written in the NFS XDR data format, so
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that any machine which supports XDR should be able to read them. The
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dump group must be <I>all</I> for the <I>xtc</I> style. The <I>unwrap</I> option of
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the <A HREF = "dump_modify.html">dump_modify</A> command allows XTC coordinates to
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be written "unwrapped" by the image flags for each atom. Unwrapped
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means that if the atom has passed thru a periodic boundary one or more
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times, the value is printed for what the coordinate would be if it had
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not been wrapped back into the periodic box. Note that these
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coordinates may thus be far outside the box size stored with the
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snapshot.
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</P>
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<P>The <I>xyz</I> style writes XYZ files, which is a simple text-based
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coordinate format that many codes can read.
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@ -310,12 +324,14 @@ some machines may not support the lo-level XDR data format that XTC
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files are written with, which will result in a compile-time error when
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a lo-level include file is not found. Putting this style in a package
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makes it easy to exclude from a LAMMPS build for those machines.
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</P>
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<P>Some pair potentials do not allow the calculation of per-atom energy
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and stress via the <I>epair</I>, <I>etotal</I>, <I>sxx</I>, etc keywords. One of
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these are the granular pair potentials. However, for those
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potentials, the <A HREF = "fix_gran_diag.html">fix gran/diag</A> command can be used
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instead.
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However, the XTC package also includes two compatibility header files
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and associated functions, which should be a suitable substitute on
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machines that do not have the appropriate native header files. This
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option can be invoked at build time by adding -DLAMMPS_XDR to the
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CCFLAGS variable in the appropriate lo-level Makefile,
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e.g. src/MAKE/Makefile.foo. This compatability mode has been tested
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successfully on Cray XT3 and IBM BlueGene/L machines and should also
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work on the Cray XT4, IBM BG/P, and Windows XP machines.
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</P>
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<P><B>Related commands:</B>
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</P>
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44
doc/dump.txt
44
doc/dump.txt
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@ -21,8 +21,7 @@ args = list of arguments for a particular style :l
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{atom} args = none
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{bond} args = none
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{dcd} args = none
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{xtc} args = precision (optional)
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precision = power-of-10 value from 10 to 1000000 (default = 1000)
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{xtc} args = none
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{xyz} args = none
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{custom} args = list of atom attributes
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possible attributes = tag, mol, type,
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@ -128,16 +127,31 @@ below.
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The {dcd} style writes DCD files, a standard atomic trajectory format
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used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD
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files are binary and thus may not be portable to different machines.
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The dump group must be {all} for the {dcd} style.
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The dump group must be {all} for the {dcd} style. The {unwrap} option
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of the "dump_modify"_dump_modify.html command allows DCD coordinates
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to be written "unwrapped" by the image flags for each atom. Unwrapped
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means that if the atom has passed thru a periodic boundary one or more
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times, the value is printed for what the coordinate would be if it had
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not been wrapped back into the periodic box. Note that these
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coordinates may thus be far outside the box size stored with the
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snapshot.
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The {xtc} style writes XTC files, a compressed trajectory format used
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by the GROMACS molecular dynamics package, and described
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"here"_http://www.gromacs.org/documentation/reference_3.3/online/xtc.html.
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The precision used in XTC files can be specified; for example, a value
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of 100 means that coordinates are stored to 1/100 nanometer accuracy.
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XTC files are portable binary files written in the NFS XDR data
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format, so that any machine which supports XDR should be able to read
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them. The dump group must be {all} for the {xtc} style.
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The precision used in XTC files can be adjusted via the
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"dump_modify"_dump_modify.html command. The default value of 1000
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means that coordinates are stored to 1/1000 nanometer accuracy. XTC
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files are portable binary files written in the NFS XDR data format, so
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that any machine which supports XDR should be able to read them. The
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dump group must be {all} for the {xtc} style. The {unwrap} option of
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the "dump_modify"_dump_modify.html command allows XTC coordinates to
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be written "unwrapped" by the image flags for each atom. Unwrapped
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means that if the atom has passed thru a periodic boundary one or more
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times, the value is printed for what the coordinate would be if it had
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not been wrapped back into the periodic box. Note that these
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coordinates may thus be far outside the box size stored with the
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snapshot.
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The {xyz} style writes XYZ files, which is a simple text-based
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coordinate format that many codes can read.
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@ -300,12 +314,14 @@ some machines may not support the lo-level XDR data format that XTC
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files are written with, which will result in a compile-time error when
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a lo-level include file is not found. Putting this style in a package
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makes it easy to exclude from a LAMMPS build for those machines.
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Some pair potentials do not allow the calculation of per-atom energy
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and stress via the {epair}, {etotal}, {sxx}, etc keywords. One of
|
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these are the granular pair potentials. However, for those
|
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potentials, the "fix gran/diag"_fix_gran_diag.html command can be used
|
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instead.
|
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However, the XTC package also includes two compatibility header files
|
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and associated functions, which should be a suitable substitute on
|
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machines that do not have the appropriate native header files. This
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option can be invoked at build time by adding -DLAMMPS_XDR to the
|
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CCFLAGS variable in the appropriate lo-level Makefile,
|
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e.g. src/MAKE/Makefile.foo. This compatability mode has been tested
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successfully on Cray XT3 and IBM BlueGene/L machines and should also
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work on the Cray XT4, IBM BG/P, and Windows XP machines.
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[Related commands:]
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@ -19,14 +19,16 @@
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<LI>one or more keyword/value pairs may be appended
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<LI>keyword = <I>format</I> or <I>scale</I> or <I>image</I> or <I>header</I> or <I>flush</I> or <I>region</I> or <I>thresh</I>
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<LI>keyword = <I>format</I> or <I>scale</I> or <I>image</I> or <I>flush</I> or <I>unwrap</I> or <I>every</I> or <I>precision</I> or <I>region</I> or <I>thresh</I>
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<PRE> <I>format</I> arg = C-style format string for one line of output
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<I>scale</I> arg = <I>yes</I> or <I>no</I>
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<I>image</I> arg = <I>yes</I> or <I>no</I>
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<I>flush</I> arg = <I>yes</I> or <I>no</I>
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<I>unwrap</I> arg = <I>yes</I> or <I>no</I>
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<I>every</I> arg = N
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N = dump every this many timesteps
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<I>precision</I> arg = power-of-10 value from 10 to 1000000
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<I>region</I> arg = region-ID or "none"
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<I>thresh</I> args = attribute operation value
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attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
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@ -41,7 +43,8 @@
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</P>
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<PRE>dump_modify 1 format "%d %d %20.15g %g %g" scale yes
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dump_modify myDump image yes scale no flush yes
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dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
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dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
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dump_modify xtcdump precision 10000
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</PRE>
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<P><B>Description:</B>
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</P>
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@ -76,10 +79,23 @@ the output in that file is current (no buffering by the OS), even if
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LAMMPS halts before the simulation completes. Flushes cannot be
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performed with dump style <I>xtc</I>.
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</P>
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<P>The <I>unwrap</I> option only applies to the dump <I>dcd</I> and <I>xtc</I> styles.
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If set to <I>yes</I>, coordinates will be written "unwrapped" by the image
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flags for each atom. Unwrapped means that if the atom has passed thru
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a periodic boundary one or more times, the value is printed for what
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the coordinate would be if it had not been wrapped back into the
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periodic box. Note that these coordinates may thus be far outside the
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box size stored with the snapshot.
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</P>
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<P>The <I>every</I> option changes the dump frequency originally specified by
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the <A HREF = "dump.html">dump</A> command to a new value which must be > 0. The
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dump frequency cannot be changed for the dump <I>dcd</I> style.
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</P>
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<P>The <I>precision</I> option only applies to the dump <I>xtc</I> style. A
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specified value of N means that coordinates are stored to 1/N
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nanometer accuracy, e.g. for N = 1000, the coordinates are written to
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1/1000 nanometer accuracy.
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</P>
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<P>The <I>region</I> keyword only applies to the dump <I>custom</I> style. If
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specified, only atoms in the region will be written to the dump file.
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Only one region can be applied as a filter (the last one specified).
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@ -109,6 +125,8 @@ whose energy is above some threshhold.
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</P>
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<P>The option defaults are format = %d and %g for each integer or
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floating point value, scale = yes, image = no, flush = yes (except for
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dump <I>xtc</I> style), region = none, and thresh = none.
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the dump <I>xtc</I> style), unwrap = no, every = whatever it was set to via
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the <A HREF = "dump.html">dump</A> command, precision = 1000, region = none, and
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thresh = none.
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</P>
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</HTML>
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@ -14,13 +14,15 @@ dump_modify dump-ID keyword values ... :pre
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dump-ID = ID of dump to modify :ulb,l
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one or more keyword/value pairs may be appended :l
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keyword = {format} or {scale} or {image} or {header} or {flush} or {region} or {thresh} :l
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keyword = {format} or {scale} or {image} or {flush} or {unwrap} or {every} or {precision} or {region} or {thresh} :l
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{format} arg = C-style format string for one line of output
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{scale} arg = {yes} or {no}
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{image} arg = {yes} or {no}
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{flush} arg = {yes} or {no}
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{unwrap} arg = {yes} or {no}
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{every} arg = N
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N = dump every this many timesteps
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{precision} arg = power-of-10 value from 10 to 1000000
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{region} arg = region-ID or "none"
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{thresh} args = attribute operation value
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attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
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@ -34,7 +36,8 @@ keyword = {format} or {scale} or {image} or {header} or {flush} or {region} or {
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dump_modify 1 format "%d %d %20.15g %g %g" scale yes
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dump_modify myDump image yes scale no flush yes
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dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2 :pre
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dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
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dump_modify xtcdump precision 10000 :pre
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[Description:]
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@ -69,10 +72,23 @@ the output in that file is current (no buffering by the OS), even if
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LAMMPS halts before the simulation completes. Flushes cannot be
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performed with dump style {xtc}.
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The {unwrap} option only applies to the dump {dcd} and {xtc} styles.
|
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If set to {yes}, coordinates will be written "unwrapped" by the image
|
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flags for each atom. Unwrapped means that if the atom has passed thru
|
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a periodic boundary one or more times, the value is printed for what
|
||||
the coordinate would be if it had not been wrapped back into the
|
||||
periodic box. Note that these coordinates may thus be far outside the
|
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box size stored with the snapshot.
|
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|
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The {every} option changes the dump frequency originally specified by
|
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the "dump"_dump.html command to a new value which must be > 0. The
|
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dump frequency cannot be changed for the dump {dcd} style.
|
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|
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The {precision} option only applies to the dump {xtc} style. A
|
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specified value of N means that coordinates are stored to 1/N
|
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nanometer accuracy, e.g. for N = 1000, the coordinates are written to
|
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1/1000 nanometer accuracy.
|
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|
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The {region} keyword only applies to the dump {custom} style. If
|
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specified, only atoms in the region will be written to the dump file.
|
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Only one region can be applied as a filter (the last one specified).
|
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|
|
@ -102,4 +118,6 @@ whose energy is above some threshhold.
|
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|
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The option defaults are format = %d and %g for each integer or
|
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floating point value, scale = yes, image = no, flush = yes (except for
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dump {xtc} style), region = none, and thresh = none.
|
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the dump {xtc} style), unwrap = no, every = whatever it was set to via
|
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the "dump"_dump.html command, precision = 1000, region = none, and
|
||||
thresh = none.
|
||||
|
|
|
|||
Loading…
Reference in New Issue